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Items: 28

1.

Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.

Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M.

Nat Immunol. 2019 Oct;20(10):1372-1380. doi: 10.1038/s41590-019-0471-5. Epub 2019 Aug 26.

PMID:
31451789
2.

Conserved phosphorylation hotspots in eukaryotic protein domain families.

Strumillo MJ, Oplová M, Viéitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P.

Nat Commun. 2019 Apr 29;10(1):1977. doi: 10.1038/s41467-019-09952-x.

3.

iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.

Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N.

G3 (Bethesda). 2019 Jan 9;9(1):1-11. doi: 10.1534/g3.118.200637.

4.

Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.

Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A.

ACS Cent Sci. 2017 Oct 25;3(10):1086-1095. doi: 10.1021/acscentsci.7b00269. Epub 2017 Aug 30.

5.

Correction to 'Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering'.

Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V.

R Soc Open Sci. 2016 Dec 14;3(12):160895. doi: 10.1098/rsos.160895. eCollection 2016 Dec.

6.

Evolution of protein phosphorylation across 18 fungal species.

Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.

Science. 2016 Oct 14;354(6309):229-232.

PMID:
27738172
7.

Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.

Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V.

R Soc Open Sci. 2016 Mar 16;3(3):150484. doi: 10.1098/rsos.150484. eCollection 2016 Mar. Erratum in: R Soc Open Sci. 2016 Dec 14;3(12 ):160895.

8.

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.

Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D.

PLoS One. 2015 Jun 15;10(6):e0130600. doi: 10.1371/journal.pone.0130600. eCollection 2015.

9.

Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited.

Rossier BC, Baker ME, Studer RA.

Physiol Rev. 2015 Jan;95(1):297-340. doi: 10.1152/physrev.00011.2014. Review.

10.

Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.

Baker ME, Nelson DR, Studer RA.

J Steroid Biochem Mol Biol. 2015 Jul;151:12-24. doi: 10.1016/j.jsbmb.2014.10.020. Epub 2014 Nov 3. Review.

PMID:
25445914
11.

CATH: comprehensive structural and functional annotations for genome sequences.

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.

Nucleic Acids Res. 2015 Jan;43(Database issue):D376-81. doi: 10.1093/nar/gku947. Epub 2014 Oct 27.

12.

Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.

Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R.

Open Biol. 2014 Oct;4(10). pii: 140121. doi: 10.1098/rsob.140121.

13.

Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations.

Rallapalli PM, Orengo CA, Studer RA, Perkins SJ.

Mol Biol Evol. 2014 Nov;31(11):3040-56. doi: 10.1093/molbev/msu248. Epub 2014 Aug 25.

14.

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

Studer RA, Christin PA, Williams MA, Orengo CA.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2223-8. doi: 10.1073/pnas.1310811111. Epub 2014 Jan 27.

15.

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.

Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.

Nucleic Acids Res. 2014 Jan;42(Database issue):D240-5. doi: 10.1093/nar/gkt1205. Epub 2013 Nov 21.

16.

Selectome update: quality control and computational improvements to a database of positive selection.

Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.

Nucleic Acids Res. 2014 Jan;42(Database issue):D917-21. doi: 10.1093/nar/gkt1065. Epub 2013 Nov 12.

17.

Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.

Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L.

PLoS Genet. 2013;9(8):e1003730. doi: 10.1371/journal.pgen.1003730. Epub 2013 Aug 15.

18.

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes.

Studer RA, Dessailly BH, Orengo CA.

Biochem J. 2013 Feb 1;449(3):581-94. doi: 10.1042/BJ20121221. Review.

PMID:
23301657
19.

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.

Nucleic Acids Res. 2013 Jan;41(Database issue):D490-8. doi: 10.1093/nar/gks1211. Epub 2012 Nov 29.

20.

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.

PLoS Comput Biol. 2012;8(5):e1002514. doi: 10.1371/journal.pcbi.1002514. Epub 2012 May 17.

21.

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport.

Studer RA, Person E, Robinson-Rechavi M, Rossier BC.

Physiol Genomics. 2011 Jul 14;43(13):844-54. doi: 10.1152/physiolgenomics.00002.2011. Epub 2011 May 10.

PMID:
21558422
22.

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Studer RA, Robinson-Rechavi M.

Mol Biol Evol. 2010 Nov;27(11):2618-27. doi: 10.1093/molbev/msq149. Epub 2010 Jun 15.

23.

Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.

Burri R, Salamin N, Studer RA, Roulin A, Fumagalli L.

Mol Biol Evol. 2010 Oct;27(10):2360-74. doi: 10.1093/molbev/msq120. Epub 2010 May 12.

PMID:
20463048
24.

Evidence for an episodic model of protein sequence evolution.

Studer RA, Robinson-Rechavi M.

Biochem Soc Trans. 2009 Aug;37(Pt 4):783-6. doi: 10.1042/BST0370783. Review.

PMID:
19614594
25.

How confident can we be that orthologs are similar, but paralogs differ?

Studer RA, Robinson-Rechavi M.

Trends Genet. 2009 May;25(5):210-6. doi: 10.1016/j.tig.2009.03.004. Epub 2009 Apr 14.

PMID:
19368988
26.

Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.

Iwema T, Chaumot A, Studer RA, Robinson-Rechavi M, Billas IM, Moras D, Laudet V, Bonneton F.

Mol Biol Evol. 2009 Apr;26(4):753-68. doi: 10.1093/molbev/msn302. Epub 2009 Jan 6.

PMID:
19126866
27.

Selectome: a database of positive selection.

Proux E, Studer RA, Moretti S, Robinson-Rechavi M.

Nucleic Acids Res. 2009 Jan;37(Database issue):D404-7. doi: 10.1093/nar/gkn768. Epub 2008 Oct 28.

28.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

Studer RA, Penel S, Duret L, Robinson-Rechavi M.

Genome Res. 2008 Sep;18(9):1393-402. doi: 10.1101/gr.076992.108. Epub 2008 Jun 18.

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